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9iip

Fucokinase part of FKP with beta-L-fucose 1-phosphate

Method: X-RAY DIFFRACTION Dmax: 72.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

L-fucokinase/L-fucose-1-P guanylyltransferase

Bacteroides fragilis

UniProt Q58T34

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 531–949 Fragment：fucokinase part ED6 6-deoxy-1-O-phosphono-beta-L-galactopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, Trypton, HEPES, beta-L-fucose 1-phosphate, MnCl2 Resolution 2.45 Å R-free 0.217

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9IIP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5YYS Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (FKP)in Bacteroides fragilis Deposited 2017-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Chain C 1–949（949 aa）
Chain D 1–949（949 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9IIS GDP-fucose pyrophosphorylase part of FKP with a SUMO tag Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–496（496 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, ammonium acetate, HEPES
Resolution 2.36 Å R-free 0.254
9IIT Full length structure of FKP in complex with GTP and GDP Deposited 2024-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–949（949 aa）
Chain B 1–949（949 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 6 FMT FORMIC ACID × 4 MLA MALONIC ACID × 2 GOL GLYCEROL × 8 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；8% Tascimate, 20% PEG 3350, 15mM GTP, 15mM MgCl2
Resolution 2.30 Å R-free 0.232

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q58T34_BACFG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–419； UniProt 531–949

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9iip

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9iip
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9iip
Deposition date deposition_date2024-06-21
Structure title titleFucokinase part of FKP with beta-L-fucose 1-phosphate
Keywords keywordsfucose, kinase, beta-L-fucose 1-phosphate, product, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.92 Å
Radius of gyration Rg (electron density) rg_electron21.33 Å
Forward intensity I(0) i049365700.00
Molecular weight molecular_weight36788.0 kDa
Excluded volume excluded_volume35701 ų
Envelope volume envelope_volume57026 ų
Hydration-shell volume shell_volume22546 ų
Envelope diameter envelope_diameter73.8 Å
Shell Rg shell_rg27.90 Å
Envelope Rg envelope_rg21.56 Å
Shape Rg shape_rg21.32 Å
Total Rg total_rg21.95 Å
Total atoms total_atoms2790
Residues n_residues361
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax72.8 Å
Rg (real space) rg_real21.92 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real4.9370e+07
I(0) uncertainty (real space) i0_real_error7.1560e+05
Rg (reciprocal space) rg_reciprocal21.92 Å
I(0) (reciprocal space) i0_reciprocal49370000.0000
Solution quality estimate total_estimate0.8781
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9 Å
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.352
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12160000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.942
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)